Hi Margo,
you should be using the talairach.lta file created by mri_em_register
(not the talairach.xfm that you have in your command line).
cheers,
Bruce
On Thu, 22 Dec 2005, Margo McKenna Benoit wrote:
Hello,
I am having a problem with the mri_ca_normalize step in autorecon2. When I
run autorecon2 (in the dev version: recon-all-nmr -subjid avm004 -autorecon2
-nosubcortseg -hemi lh), it gives me a message that norm.mgz is missing, and
it seems that the files are not being created (either in the <subjid>/mri
/norm folder or in norm.mgz format). I tried running mri_ca_normalize alone
with the following command:
"mri_ca_normalize -mask avm004/mri/brain.mgz avm004/mri/nu.mgz
${FREESURFER_HOME}/average/RB40_talairach_2005-07-20.gca
avm004/mri/transforms/talairach.xfm avm004/mri/norm.mgz"
and I get the following output, still with no norm.mgz or norm files:
reading atlas from
'/usr/local/freesurfer/dev/average/RB40_talairach_2005-07-20.gca'...
setting gca type = Normal gca type
reading transform from 'avm004/mri/transforms/talairach.xfm'...
reading input volume from avm004/mri/nu.mgz...
Note: program considers input volume #1 as the most T1-like
using real data threshold=53.0
using (111, 120, 127) as brain centroid...
mean wm in atlas = 110, using box (97,105,108) --> (125, 135,146) to find MRI
wm
before smoothing, mri peak at 184
after smoothing, mri peak at 184, scaling input intensities by 0.596
scaling channel 0 by 0.596172
using 269906 sample points...
INFO: transform used
GCApriorToSourceVoxelFloat: needs vox-to-vox transform
Is there some way to get the normalize step to run during autorecon2?
Thanks for your help,
Margo
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